How to dynamically access data from NCBI database using biojava?
why do you need BioJava ? A simple call with java.net.URL is enough.
I am sure new Biojava (3.0+) implements some methods, but I had a good experience fetching sequences with 1.8.2 version using RichSequenceDB class http://www.biojava.org/docs/api1.8.2/org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html. You'll need to instantiate the class and use the getRichSequence("accession") method. Also, NCBI provides an advanced toolkit for Java using Axis2: http://www.ncbi.nlm.nih.gov/books/NBK55696/.
I always use R package named as GEOquery to get data from NCBI.
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